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libsbml.RDFAnnotationParser Class Reference
Inheritance diagram for libsbml.RDFAnnotationParser:
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Detailed Description

{core}

Read/write/manipulate RDF annotations stored in SBML annotation elements.

This class of objects is defined by libSBML only and has no direct equivalent in terms of SBML components. This class is not prescribed by the SBML specifications, although it is used to implement features defined in SBML.

RDFAnnotationParser is a libSBML construct used as part of the libSBML support for annotations conforming to the guidelines specified by MIRIAM ('Minimum Information Requested in the Annotation of biochemical Models', Nature Biotechnology, vol. 23, no. 12, Dec. 2005). Section 6 of the SBML Level 2 and Level 3 specification documents defines a recommended way of encoding MIRIAM information using a subset of RDF (Resource Description Format). The general scheme is as follows. A set of RDF-based annotations attached to a given SBML <annotation> element are read by RDFAnnotationParser and converted into a list of CVTerm objects. There are different versions of the main method, and RDFAnnotationParser.parseRDFAnnotation(), used depending on whether the annotation in question concerns the MIRIAM model history or other MIRIAM resource annotations. A special object class, ModelHistory, is used to make it easier to manipulate model history annotations.

All of the methods on RDFAnnotationParser are static; the class exists only to encapsulate the annotation and CVTerm parsing and manipulation functionality.

Public Member Functions

def createAnnotation
 
def createCVTerms
 
def createRDFAnnotation
 
def deleteRDFAnnotation
 
def deleteRDFCVTermAnnotation
 
def deleteRDFHistoryAnnotation
 
def parseCVTerms
 
def parseModelHistory
 
def parseOnlyModelHistory
 
def parseRDFAnnotation
 

Member Function Documentation

def libsbml.RDFAnnotationParser.createAnnotation ( )

{core}

Read/write/manipulate RDF annotations stored in SBML annotation elements.

This class of objects is defined by libSBML only and has no direct equivalent in terms of SBML components. This class is not prescribed by the SBML specifications, although it is used to implement features defined in SBML.

RDFAnnotationParser is a libSBML construct used as part of the libSBML support for annotations conforming to the guidelines specified by MIRIAM ('Minimum Information Requested in the Annotation of biochemical Models', Nature Biotechnology, vol. 23, no. 12, Dec. 2005). Section 6 of the SBML Level 2 and Level 3 specification documents defines a recommended way of encoding MIRIAM information using a subset of RDF (Resource Description Format). The general scheme is as follows. A set of RDF-based annotations attached to a given SBML <annotation> element are read by RDFAnnotationParser and converted into a list of CVTerm objects. There are different versions of the main method, and RDFAnnotationParser.parseRDFAnnotation(), used depending on whether the annotation in question concerns the MIRIAM model history or other MIRIAM resource annotations. A special object class, ModelHistory, is used to make it easier to manipulate model history annotations.

All of the methods on RDFAnnotationParser are static; the class exists only to encapsulate the annotation and CVTerm parsing and manipulation functionality. Python method signature(s):

createAnnotation()   XMLNode

Creates a blank annotation and returns its root XMLNode object.

This creates a completely empty SBML <annotation> element. It is not attached to any SBML element. An example of how this might be used is illustrated in the following code fragment. In this example, suppose that content is an XMLNode object previously created, containing MIRIAM-style annotations, and that sbmlObject is an SBML object derived from SBase (e.g., a Model, or a Species, or a Compartment, etc.). Then:

RDF     = RDFAnnotationParser.createRDFAnnotation() # Create RDF annotation XML structure.
success = RDF.addChild(...content...)               # Put some content into it.
...                                                 # Check 'success' return code value.

annot   = RDFAnnotationParser.createAnnotation()    # Create <annotation> container.
success = annot.addChild(RDF)                       # Put the RDF annotation into it.
...                                                 # Check 'success' return code value.

success = sbmlObject.setAnnotation(annot)           # Set object's annotation to what we built.
...                                                 # Check 'success' return code value.

The SBML specification contains more information about the format of annotations. We urge readers to consult Section 6 of the SBML Level 2 (Versions 2–4) and SBML Level 3 specification documents.

Returns
a pointer to an XMLNode for the annotation
Note
Because this is a static method on a class, the Python language interface for libSBML will contain two variants. One will be the expected, normal static method on the class (i.e., a regular methodName), and the other will be a standalone top-level function with the name ClassName_methodName(). This is merely an artifact of how the language interfaces are created in libSBML. The methods are functionally identical.
See also
RDFAnnotationParser.createRDFAnnotation()
def libsbml.RDFAnnotationParser.createCVTerms (   args)

Python method signature(s):

createCVTerms(SBase obj)   XMLNode

Takes a list of CVTerm objects and creates a the RDF 'Description' element.

This essentially takes the given SBML object, reads out the CVTerm objects attached to it, creates an RDF 'Description' element to hold the terms, and adds each term with appropriate qualifiers.

Parameters
objthe SBML object to start from
Returns
the XMLNode tree corresponding to the Description element of an RDF annotation.
Note
Because this is a static method on a class, the Python language interface for libSBML will contain two variants. One will be the expected, normal static method on the class (i.e., a regular methodName), and the other will be a standalone top-level function with the name ClassName_methodName(). This is merely an artifact of how the language interfaces are created in libSBML. The methods are functionally identical.
def libsbml.RDFAnnotationParser.createRDFAnnotation ( )

Python method signature(s):

createRDFAnnotation()   XMLNode

Creates a blank RDF element suitable for use in SBML annotations.

The annotation created by this method has namespace declarations for all the relevant XML namespaces used in RDF annotations and also has an empty RDF element. The result is the following XML:

<rdf:RDF xmlns:rdf='http://www.w3.org/1999/02/22-rdf-syntax-ns#'
 xmlns:dc='http://purl.org/dc/elements/1.1/'
 xmlns:dcterms='http://purl.org/dc/terms/'
 xmlns:vCard='http://www.w3.org/2001/vcard-rdf/3.0#'
 xmlns:bqbiol='http://biomodels.net/biology-qualifiers/'
 xmlns:bqmodel='http://biomodels.net/model-qualifiers/' >

</rdf:RDF>

Note that this does not create the containing SBML <annotation> element; the method RDFAnnotationParser.createAnnotation() is available for creating the container.

Returns
a pointer to an XMLNode
Note
Because this is a static method on a class, the Python language interface for libSBML will contain two variants. One will be the expected, normal static method on the class (i.e., a regular methodName), and the other will be a standalone top-level function with the name ClassName_methodName(). This is merely an artifact of how the language interfaces are created in libSBML. The methods are functionally identical.
See also
RDFAnnotationParser.createAnnotation()
def libsbml.RDFAnnotationParser.deleteRDFAnnotation (   args)

Python method signature(s):

deleteRDFAnnotation(XMLNode annotation)   XMLNode

Deletes any SBML MIRIAM RDF annotation found in the given XMLNode tree and returns any remaining annotation content.

The name of the XMLNode given as parameter annotation must be 'annotation', or else this method returns None. The method will walk down the XML structure looking for elements that are in the RDF XML namespace, and remove them if they conform to the syntax of a History or CVTerm element.

Parameters
annotationthe XMLNode tree within which the RDF annotation is to be found and deleted
Returns
the XMLNode structure that is left after RDF annotations are deleted.
Note
Because this is a static method on a class, the Python language interface for libSBML will contain two variants. One will be the expected, normal static method on the class (i.e., a regular methodName), and the other will be a standalone top-level function with the name ClassName_methodName(). This is merely an artifact of how the language interfaces are created in libSBML. The methods are functionally identical.
def libsbml.RDFAnnotationParser.deleteRDFCVTermAnnotation (   args)

Python method signature(s):

deleteRDFCVTermAnnotation(XMLNode annotation)   XMLNode

Deletes any SBML MIRIAM RDF 'CVTerm' annotation found in the given XMLNode tree and returns any remaining annotation content.

The name of the XMLNode given as parameter annotation must be 'annotation', or else this method returns None. The method will walk down the XML structure looking for elements that are in the RDF XML namespace, and remove any that conform to the syntax of a CVTerm element.

Parameters
annotationthe XMLNode tree within which the RDF annotation is to be found and deleted
Returns
the XMLNode structure that is left after RDF annotations are deleted.
Note
Because this is a static method on a class, the Python language interface for libSBML will contain two variants. One will be the expected, normal static method on the class (i.e., a regular methodName), and the other will be a standalone top-level function with the name ClassName_methodName(). This is merely an artifact of how the language interfaces are created in libSBML. The methods are functionally identical.
def libsbml.RDFAnnotationParser.deleteRDFHistoryAnnotation (   args)

Python method signature(s):

deleteRDFHistoryAnnotation(XMLNode annotation)   XMLNode

Deletes any SBML MIRIAM RDF 'History' annotation found in the given XMLNode tree and returns any remaining annotation content.

The name of the XMLNode given as parameter annotation must be 'annotation', or else this method returns None. The method will walk down the XML structure looking for elements that are in the RDF XML namespace, and remove any that conform to the syntax of a History element.

Parameters
annotationthe XMLNode tree within which the RDF annotation is to be found and deleted
Returns
the XMLNode structure that is left after RDF annotations are deleted.
Note
Because this is a static method on a class, the Python language interface for libSBML will contain two variants. One will be the expected, normal static method on the class (i.e., a regular methodName), and the other will be a standalone top-level function with the name ClassName_methodName(). This is merely an artifact of how the language interfaces are created in libSBML. The methods are functionally identical.
def libsbml.RDFAnnotationParser.parseCVTerms (   args)

Python method signature(s):

parseCVTerms(SBase obj)   XMLNode

Takes a list of CVTerm objects and creates a complete SBML annotation around it.

This essentially takes the given SBML object, reads out the CVTerm objects attached to it, callsRDFAnnotationParser.createRDFAnnotation() to create an RDF annotation to hold the terms, and finally callsRDFAnnotationParser.createAnnotation() to wrap the result as an SBML <annotation> element.

Parameters
objthe SBML object to start from
Returns
the XMLNode tree corresponding to the annotation.
Note
Because this is a static method on a class, the Python language interface for libSBML will contain two variants. One will be the expected, normal static method on the class (i.e., a regular methodName), and the other will be a standalone top-level function with the name ClassName_methodName(). This is merely an artifact of how the language interfaces are created in libSBML. The methods are functionally identical.
def libsbml.RDFAnnotationParser.parseModelHistory (   args)

Python method signature(s):

parseModelHistory(SBase obj)   XMLNode

Reads the model history and cvTerms stored in obj and creates the XML structure for an SBML annotation representing that metadata if there is a model history stored in obj.

Parameters
objany SBase object
Returns
the XMLNode corresponding to an annotation containing MIRIAM-compliant model history and CV term information in RDF format.
Note
If the object does not have a history element stored then None is returned even if CVTerms are present.
Because this is a static method on a class, the Python language interface for libSBML will contain two variants. One will be the expected, normal static method on the class (i.e., a regular methodName), and the other will be a standalone top-level function with the name ClassName_methodName(). This is merely an artifact of how the language interfaces are created in libSBML. The methods are functionally identical.
def libsbml.RDFAnnotationParser.parseOnlyModelHistory (   args)

Python method signature(s):

parseOnlyModelHistory(SBase obj)   XMLNode

Reads the model history stored in obj and creates the XML structure for an SBML annotation representing that history.

Parameters
objany SBase object
Returns
the XMLNode corresponding to an annotation containing MIRIAM-compliant model history information in RDF format.
Note
Because this is a static method on a class, the Python language interface for libSBML will contain two variants. One will be the expected, normal static method on the class (i.e., a regular methodName), and the other will be a standalone top-level function with the name ClassName_methodName(). This is merely an artifact of how the language interfaces are created in libSBML. The methods are functionally identical.
def libsbml.RDFAnnotationParser.parseRDFAnnotation (   args)

Python method signature(s):

parseRDFAnnotation(XMLNode annotation, char * metaId=None, XMLInputStream stream=None)   ModelHistory
parseRDFAnnotation(XMLNode annotation, char * metaId=None)   ModelHistory
parseRDFAnnotation(XMLNode annotation)   ModelHistory
parseRDFAnnotation(XMLNode annotation, CVTermList CVTerms)
parseRDFAnnotation(XMLNode annotation, CVTermList CVTerms, char * metaId=None, XMLInputStream stream=None)
parseRDFAnnotation(XMLNode annotation, CVTermList CVTerms, char * metaId=None)

This method has multiple variants that differ in the arguments they accept. Each is described separately below.


Method variant with the following signature:
parseRDFAnnotation(XMLNodeannotation, List *CVTerms, string metaId = None, XMLInputStream stream = None)

Parses an annotation (given as an XMLNode tree) into a list of CVTerm objects.

This is used to take an annotation that has been read into an SBML model, identify the RDF elements within it, and create a list of corresponding CVTerm (controlled vocabulary term) objects.

Parameters
annotationXMLNode containing the annotation.
CVTermslist of CVTerm objects to be created.
metaIdoptional metaId, if set only the RDF annotation for this metaId will be returned.
streamoptional XMLInputStream that facilitates error logging.
Note
Because this is a static method on a class, the Python language interface for libSBML will contain two variants. One will be the expected, normal static method on the class (i.e., a regular methodName), and the other will be a standalone top-level function with the name ClassName_methodName(). This is merely an artifact of how the language interfaces are created in libSBML. The methods are functionally identical.

Method variant with the following signature:
parseRDFAnnotation(XMLNodeannotation, string metaId = None, XMLInputStream stream = None)

Parses an annotation into a ModelHistory class instance.

This is used to take an annotation that has been read into an SBML model, identify the RDF elements representing model history information, and create a list of corresponding CVTerm objects.

Parameters
annotationXMLNode containing the annotation.
streamoptional XMLInputStream that facilitates error logging
metaIdoptional metaId, if set only the RDF annotation for this metaId will be returned.
Note
Because this is a static method on a class, the Python language interface for libSBML will contain two variants. One will be the expected, normal static method on the class (i.e., a regular methodName), and the other will be a standalone top-level function with the name ClassName_methodName(). This is merely an artifact of how the language interfaces are created in libSBML. The methods are functionally identical.
Returns
a pointer to the ModelHistory created.